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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Amino Acid Residues Controlling Domain Interaction and Interdomain Electron Transfer in Cellobiose Dehydrogenase

The function of cellobiose dehydrogenase (CDH) in biosensors, biofuel cells, and as a physiological redox partner of lytic polysaccharide monooxygenase (LPMO) is based on its role as an electron donor. Before donating electrons to LPMO or electrodes, an interdomain electron transfer from the catalytic FAD-containing dehydrogenase domain to the electron shuttling cytochrome domain of CDH is required. This study investigates the role of two crucial amino acids located at the dehydrogenase domain on domain interaction and interdomain electron transfer by structure-based engineering. The electron transfer kinetics of wild-type Myriococcum thermophilum CDH and its variants M309A, R698S, and M309A/R698S were analyzed by stopped-flow spectrophotometry and structural effects were studied by small-angle X-ray scattering. The data show that R698 is essential to pull the cytochrome domain close to the dehydrogenase domain and orient the heme propionate group towards the FAD, while M309 is an integral part of the electron transfer pathway – its mutation reducing the interdomain electron transfer 10-fold. Structural models and molecular dynamics simulations pinpoint the action of these two residues on the domain interaction and interdomain electron transfer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Solving the puzzle of Fe homeostasis by integrating molecular, mathematical, and societal models

To ensure optimal utilization and bioavailability, iron uptake, transport, subcellular localization, and assimilation are tightly regulated in plants. In this work, we examine recent advances in our understanding of cellular responses to Fe deficiency. We then use intracellular mechanisms of Fe homeostasis to discuss how formalizing cell biology knowledge via a mathematical model can advance discovery even when quantitative data is limited. Using simulation-based inference to identify plausible systems mechanisms that conform to known emergent phenotypes can yield novel, testable hypotheses to guide targeted experiments. However, this approach relies on the accurate encoding of domain-expert knowledge in exploratory mathematical models. We argue that this would be facilitated by fostering more “systems thinking” life scientists and that diversifying your research team may be a practical path to achieve that goal.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Solvent and Temperature Effects on Photoinduced Proton-Coupled Electron Transfer in the Marcus Inverted Region

Concerted proton-coupled electron transfer (PCET) in the Marcus inverted region was recently demonstrated. Understanding the requirements for such reactivity is fundamentally important and holds promise as a design principle for solar energy conversion systems. Herein, we investigate the solvent polarity and temperature dependence of photoinduced proton-coupled charge separation (CS) and charge recombination (CR) in anthracene–phenol–pyridine triads: 1 (10-(4-hydroxy-3-(4-methylpyridin-2-yl)benzyl)anthracene-9-carbonitrile) and 2 (10-(4-hydroxy-3-(4-methoxypyridin-2-yl)benzyl)anthracene-9-carbonitrile). Both the CS and CR rate constants increased with increasing polarity in acetonitrile:n-butyronitrile mixtures. The kinetics were semi-quantitatively analyzed where changes in dielectric and refractive index, and thus consequently changes in driving force (–ΔG°) and reorganization energy (λ), were accounted for. The results were further validated by fitting the temperature dependence, from 180 to 298 K, in n-butyronitrile. The analyses support previous computational work where transitions to proton vibrational excited states dominate the CR reaction with a distinct activation free energy (ΔG* CR ~ 140 meV). However, the solvent continuum model fails to accurately describe the changes in ΔG° and λ with temperature via changes in dielectric constant and refractive index. Satisfactory modeling was obtained using the results of a molecular solvent model, which predicts that λ decreases with temperature, opposite to that of the continuum model. To further assess the solvent polarity control in the inverted region, the reactions were studied in toluene. Nonpolar solvents decrease both ΔG° CR and λ, slowing CR into the nanosecond time regime for 2 in toluene at 298 K. This demonstrates how PCET in the inverted region may be controlled to potentially use proton-coupled CS states for efficient solar fuel production and photoredox catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

A Bayesian Calibration Framework with Embedded Model Error for Model Diagnostics

We study the utility and performance of a Bayesian model error embedding construction in the context of molecular dynamics modeling of metallic alloys, where we embed model error terms in existing interatomic potential model parameters. To alleviate the computational burden of this approach, we propose a framework combining likelihood approximation and Gaussian process surrogates. Here we leverage sparse Gaussian process techniques to construct a hierarchy of increasingly accurate but more expensive surrogate models. This hierarchy is then exploited by multilevel Markov chain Monte Carlo methods to efficiently sample from the target posterior distribution. We illustrate the utility of this approach by calibrating an interatomic potential model for a family of gold-copper alloys. In particular, this case study highlights effective means for dealing with computational challenges with Bayesian model error embedding in large-scale physical models, and the utility of embedded model error for model diagnostics.

Bayesian inference↗
DOE OSTI2025

Extended molecular eigenmodes treatment of dipole–dipole NMR relaxation in real fluids

Traditional models of NMR relaxation fail to account for the complex, multi-exponential behavior of the autocorrelation function in realistic systems characterized by soft-interactions and molecules that are chemically and physically complex. Here, in this study, we describe the relative diffusion of the spin dipoles by means of a Fokker–Planck equation that includes an interaction potential of mean force to account for the response of the physical/chemical environment around the dipoles. By numerically solving the Fokker–Planck equation for the diffusion propagator, we estimate dipole–dipole NMR relaxation for like- and unlike-spin systems via its eigenmode solution. We test the model against molecular simulations of diffusing dipoles with harmonic potentials and also validate using experimental longitudinal relaxation data from real systems, including Gd(III)–aqua and Gd(III)–DO3A–butrol complexes, the latter being an important MRI contrast agent. Using this novel approach, we predict both the inner- and outer-shell contributions to the relaxivity rates with excellent accuracy at frequencies relevant to MRI. We also show that, under the appropriate assumptions, our framework naturally recovers the Bloembergen–Purcell–Pound, the Solomon–Bloembergen–Morgan, and the Hwang–Freed models. Our implementation is general and publicly available for application to a broad range of systems.

Pinheiro dos Santos, Thiago J. [Rice Univ., Housto↗
DOE OSTI2022

Solvation Thermodynamics of Solutes in Water and Ionic Liquids Using the Multiscale Solvation-Layer Interface Condition Continuum Model

We report molecular assembly processes are generally driven by thermodynamic properties in solutions. Atomistic modeling can be very helpful in designing and understanding complex systems, except that bulk solvent is very inefficient to treat explicitly as discrete molecules. The SLIC/CDC multiscale model combines continuum solvent electrostatics based on the solvent layer interface condition (SLIC) with statistical thermodynamic models for hydrogen bonding and nonpolar modes: cavity formation, dispersion interactions, combinatorial mixing (CDC). The SLIC/CDC model predicts Gibbs energies of solvation for a database of 500 solutes in water with average accuracy better than 1 kcal/mol both for experimental measurements and for explicit-solvent molecular dynamics simulations. The separate SLIC/CDC energy mode values agree quantitatively with those computed from explicit-solvent molecular dynamics. The SLIC/SASA multiscale model combines the SLIC continuum electrostatic model with the solvent accessible surface area (SASA) nonpolar energy mode. The SLIC/SASA model predicts Gibbs energies of solvation with better than 1.4 kcal/mol average accuracy in aqueous systems and better than 1.6 kcal/mol average accuracy in ionic liquids. Both models predict solvation entropies, and are the first implicit-solvation models capable of predicting solvation heat capacities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Model for photothermal ionization and molecular recombination during pulsed ablation of polyethylene

The surface erosion of polyethylene is studied under conditions characteristic of extremely high-rate heating expected in laser-driven and high energy density experiments. A coupled model for photoionization and volumetric photothermal degradation of polyethylene is developed that includes finite rate chemistry and molecular recombination of radicals. First, the model is used to explore the evolution of radicals and hydrocarbons during isochoric heating, for which it is found that polyethylene is not in chemical equilibrium for rates >108K/s. Then, the model is used to explore the cooperativity between photoionization and photothermal ionization during one-dimensional ablation from a pulsed heating source, accounting for coupled energy deposition, thermokinetics, thermochemistry, hydrodynamics, mechanics, and thermal conduction in the ALEGRA multi-physics code. The ablation depth per energy pulse is found to agree with an analytical model for instantaneous energy deposition and absent molecular recombination or photoionization. Otherwise, molecular recombination of radicals reduces the depth of ablation per pulse, owing to thermal stabilization on forming branched molecules. Radical formation through photoionization can be compensated for by recombination, but it accelerates ablation at high enough photoionization rates. Finally, the influence of molecular recombination on the ablation depth is found to decrease for long pulses, owing to decreased recombination reaction rates at lower vapor densities near the ablated surface. These and other findings highlight competition between the processes of scission, recombination, and photoionization during pulsed ablation of polyethylene.

Moore, N. W. (ORCID:0000000272259674)↗
DOE OSTI2021

Numerically exact generalized Green's function cluster expansions for electron-phonon problems

We generalize the family of approximate momentum average methods to formulate a numerically exact, convergent hierarchy of equations whose solution provides an efficient algorithm to compute the Green's function of a particle dressed by bosons suitable in the entire parameter regime. We use this approach to extract ground-state properties and spectral functions. Our approximation-free framework, dubbed the generalized Green's function cluster expansion (GGCE), allows access to exact numerical results in the extreme adiabatic limit, where many standard methods struggle or completely fail. We showcase the performance of the method, specializing three important models of charge-boson coupling in solids and molecular complexes: the molecular Holstein model, which describes coupling between charge density and local distortions, the Peierls model, which describes modulation of charge hopping due to intersite distortions, and a more complex Holstein + Peierls system with couplings to two different phonon modes, paradigmatic of charge-lattice interactions in organic crystals. Furthermore, the GGCE serves as an efficient approach that can be systematically extended to different physical scenarios, thus providing a tool to model the frequency dependence of dressed particles in realistic settings.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Reaction Pathways and Energy Consumption in NH 3 Decomposition for H 2 Production by Low Temperature, Atmospheric Pressure Plasma

Pathways for NH 3 decomposition to N 2 and N 2 H 4 by atmospheric pressure nonthermal plasma are analyzed using a combination of molecular beam mass spectrometry measurements and zero-dimensional kinetic modeling. Experimental measurements show that NH 3 conversion and selectivity towards N 2 formation scale monotonically with the specific energy input into the plasma with ~ 100% selectivity to N 2 formation achieved at specific energy inputs above 0.12 J cm −3 (3.1 eV (molecule NH 3 ) −1 ). The kinetic model recovers these trends, although it underpredicts N 2 selectivity at low specific energy input. These discrepancies can be explained by the underestimation of reaction rate coefficients for reactions that consume N 2 H x species in collisions with H radicals and/or radial nonuniformities in power deposition, gas temperature, and species concentrations that are not represented by the plug flow approximation used in the model. The kinetic model shows that N 2 formation proceeds through N 2 H x decomposition pathways rather than NH x decomposition pathways in low temperature, atmospheric pressure plasma. Higher selectivity toward N 2 production can be achieved by operating at higher NH 3 conversion and with a higher gas temperature. Furthermore, the high energy cost of NH 3 decomposition by atmospheric pressure nonthermal plasma found in this work (25–50 eV (molecule NH 3 converted) −1 ; 17–33 eV (molecule H 2 formed) −1 ) is a result of the energy requirement for electron-impact dissociation of NH 3 and the significant re-formation of NH 3 by three-body recombination reactions between NH 2 and H.

Nonthermal plasma↗